test: improve integration test with dynamic mock and full coverage

tests/test_integration.py

@@ -141,8 +141,16 @@ def _make_config(vault_path: Path, vector_store_path: Path) -> Config:
 @patch("companion.rag.search.OllamaEmbedder")
 @patch("companion.rag.indexer.OllamaEmbedder")
 def test_index_and_search_flow(mock_indexer_embedder, mock_search_embedder):
+    """Verify end-to-end indexing and semantic search with mocked embeddings."""
     mock_embed = MagicMock()
-    mock_embed.embed.return_value = [[1.0, 0.0, 0.0, 0.0], [0.0, 1.0, 0.0, 0.0]]
+
+    def mock_embed_side_effect(texts):
+        return [
+            [1.0, 0.0, 0.0, 0.0] if i == 0 else [0.0, 1.0, 0.0, 0.0]
+            for i in range(len(texts))
+        ]
+
+    mock_embed.embed.side_effect = mock_embed_side_effect
     mock_indexer_embedder.return_value = mock_embed
     mock_search_embedder.return_value = mock_embed
 
@@ -171,3 +179,8 @@ def test_index_and_search_flow(mock_indexer_embedder, mock_search_embedder):
         assert len(results) >= 1
         files = {r["source_file"] for r in results}
         assert "note1.md" in files
+
+        results = engine.search("goodbye")
+        assert len(results) >= 1
+        files = {r["source_file"] for r in results}
+        assert "note2.md" in files